greymatters
We are not aware of any kind of issue like the one you are describing.
And we are using Stock Central every day ourselves, and never happened to us.
In order to discard any possible conflict with a 3rd party plugin, I'd suggest you try to disable all your plugins except WooCommerce and ATUM, and also switch to any default theme and try that way. If it works, you can start enabling them back one by one until you find the source of the conflict.
We strongly recommend you do so on a staging site, if possible.
Best Regards,
Salva.